Serving as the main connecting hub for rail traffic between Tokyo's special wards and Western Tokyo on inter-city rail, commuter rail, and metro lines, the station was used by an average of 3.64 million people per day in 2007, making it, by far, the world's busiest transport hub (and registered as such with Guinness World Records). The station has 36 platforms. Including an underground arcade, there are well over 200 exits.

The station is centered around facilities servicing the East Japan Railway Company (JR East) lines. These consist of eight ground-level island platforms (16 tracks) on a north-south axis, connected by two overhead and two underground concourses. Most JR services here are urban and suburban mass transit lines, although JR's long-distance express services to Kōfu and Matsumoto on the Chūō Main Line, Narita Express to Narita Airport, and joint operations with Tobu Railway to Nikkō and Kinugawa Onsen also use this station. The JR section alone handles an average of 1.5 million passengers a day.

The terminus for the private Odakyu Odawara Line is parallel to the JR platforms on the west side, and handles an average of 490,000 passengers daily. This is a major commuter route stretching southwest through the suburbs and out towards the coastal city of Odawara and the mountains of Hakone. The ten platforms are built on two levels beneath the Odakyu department store; three express service tracks (six platforms) on the ground level and two tracks (four platforms) on the level below. Each track has platforms on both sides in order to completely separate boarding and alighting passengers.

The Keio Line concourse is located to the west of the Odakyu line concourse, two floors below ground level under Keio department store. It consists of three platforms stretching north to south. Approximately 720,000 passengers use this section daily, which makes it the busiest amongst the non-JR Group railways of Japan. This suburban commuter line links Shinjuku to the city of Hachiōji to the west.[2] Chest-high platform edge doors were introduced on the Keio Line platforms in March 2014.[3] The doors are different colours for each platform. The doors on platform 2 are green.[3]

The shared facilities for the Toei Shinjuku subway line and the Keiō New Line consist of two platforms stretching east-west five floors beneath the Kōshū Kaidō avenue to the southwest of the JR section. The concourse is managed by Keio Corporation but is in a separate location to the main Keio platforms. Further south (and deeper underground) are the two north-to-south Toei Ōedo subway line platforms.

Many department stores and shopping malls are built directly into the station. These include

Lumine Est - above JR's east exit

Odakyu department store - above the Odakyu line concourse

Odakyu Mylord - above the southern end of Odakyu line concourse

Lumine 1 shopping mall - above the Keio Line concourse

Lumine 2 shopping mall - above JR's south and Lumine exits

Keio Department store - above the Keio Line concourse

Keio Mall - underground mall to the southwest of the Keio Line concourse

Odakyu Ace - underground malls beneath the bus terminal by the west exit.

In addition to the above, the Metro Promenade, which is an underground mall owned by Tokyo Metro, extends eastwards from the station beneath Shinjuku-dori avenue, all the way to the adjacent Shinjuku-sanchōme station with 60 exits along the way. The Metro Promenade in turn connects to Shinjuku Subnade, another underground shopping mall, which leads onto Seibu Railway's Seibu-Shinjuku station.

Shinjuku Station is connected by underground passageways and shopping malls to:

Shinjuku Station opened in 1885 as a stop on Japan Railway's Akabane-Shinagawa line (now part of the Yamanote Line). Shinjuku was still a quiet community at the time and the station was not heavily trafficked at first. The opening of the Chūō Line (1889), Keiō Line (1915) and Odakyū Line (1923) led to increasing traffic through the station. Subway service began in 1959.

In August 1967, a freight train carrying jet fuel bound for the U.S. air base in Tachikawa derailed and caught fire on the Chūō Rapid tracks.

The station was a major site for student protests in 1968 and 1969, the height of civil unrest in postwar Japan. On October 21, 1968, 290,000 marchers participated in International Anti-War Day taking over Shinjuku station and forcing trains to stop. In May and June, 1969, members of the antiwar group Beheiren carrying guitars and calling themselves "folk guerrillas" led weekly singalongs in the underground plaza outside the west exit of the station, attracting crowds of thousands. Participants described it as a "liberated zone" and a "community of encounter."[15] In July, riot police cleared the plaza with tear gas and changed signs in the station to read "West Exit Concourse" instead of "West Exit Plaza." The incident represented a significant defeat for public activism in Tokyo.

There have been plans at various points in history to connect Shinjuku into the Shinkansen network, and the 1973 Shinkansen Basic Plan, still in force, specifies that the station should be the southern terminus of the Jōetsu Shinkansen line to Niigata. While construction of the Ōmiya-Shinjuku link never started and the Jōetsu line presently terminates in Tokyo Station, the right of way, including an area underneath the station, remains reserved.

On May 5, 1995, the Aum Shinrikyodoomsday cult attempted a chemical terrorist attack by setting off a cyanide gas device in a toilet in the underground concourse, barely a month after the gas attack on the Tokyo subway which killed 13, left 6,252 people with non-fatal injuries, severely injured 50 people, and caused 984 cases of temporary vision problems. This time the attack was thwarted by staff who extinguished the burning device.

When the Keio Line extended to Shinjuku in 1915, its terminal was located several blocks east of the government railway (presently JR) station. The terminal was first named Shinjuku-Oiwake Station (新宿追分駅?) and was on the street near the Isetan department store. In 1927, the station was moved from the street to a newly built terminal adjacent to the original station. The station building housed a department store. The station name was changed to Yotsuya-Shinjuku Station (四谷新宿駅?) in 1930 and again to Keiō Shinjuku Station (京王新宿駅?) in 1937.

The tracks from the terminal were on the Kōshū Kaidō highway, which crosses the Yamanote Line and the Chūō Line in front of the south entrance of Shinjuku Station by a bridge. The Keiō Line had a station for the access to Shinjuku Station, named Teishajō-mae Station (停車場前駅?) and renamed in 1937 Shōsen Shinjuku Ekimae Station (省線新宿駅前駅?).

In July 1945, the terminal of the Keiō Line was relocated to the present location, though on the ground level, on the west side of Shinjuku Station. Keiō Shinjuku Station and Shōsen Shinjuku Ekimae Station were closed. This was because the trains faced difficulty in climbing up the slopes of the bridge over the governmental railway after one of the nearby transformer substations was destroyed by an air raid. The site of Keiō Shinjuku Station near Shinjuku-Sanchōme subway station is now occupied by two buildings owned by Keiō: Keiō Shinjuku Sanchōme Building and Keiō Shinjuku Oiwake Building.